Introduction of entrezgene XML ASN1 data structure

[smoe]

I felt a bit overwhelmed with the XML implementation bits. Maybe you can give me a helping hand / directions on those. As a consequence the tests did not test anything :-) But it all builds and does not complain too much.

[PoorRican]

I built this program for viewing the XML files which might help with navigating the actual XML file: https://github.com/PoorRican/browsr. Hopefully this solves some of your frustrations.

Just read your comment, I will see if I can get this running over the weekend.

[smoe]

I built this program for viewing the XML files which might help with navigating the actual XML file: https://github.com/PoorRican/browsr . Hopefully this solves some of your frustrations.

The context I want to give it is https://github.com/magnusmanske/gentle_rs

Did the code you implemented work for you? I would rather merge it, and create an issue for tests.

A merge should be of no harm.

I would love to have this as a fully complete library as I built this with a purpose.

As I said I am lacking the insight on what exactly is missing, but the parts I had addressed can be automated, I guess. At least this should be the case once the typical LLMs got retrained on ncbi-rs :-) I have some good confidence that anything we type here on MS-run GitHub will also be fed into MS-supported OpenAI, so if you are up to it, maybe describe explicitly in the merge commit of the PR (or here) what was missing. Most helpful for GENtle I think would now be an extension towards the Blast data structures, so I would address that next

[smoe]

I have added a considerable amount of implementation work locally - please do not also work on it. :-/ Sorry for the late warning.

[smoe]

The parsers now parse but somehow they do not do their job :-/ It is likely something stupid somewhere but I cannot find it.

[smoe]

@PoorRican May I ask for some comments from your side?

[PoorRican]

@smoe Will be working on this today. Merry Xmas.

[smoe]

Think I now at least know what my biggest problems are.

• I have ruined the parsing of dates. Did not work for me before, or I have not understood them :-) So I feel not completely bad at this very moment. Have now commented out the respective tests.
• I have a problem with parsing the numeric values of an enum. This ruins the EntrezgeneType and others.

[smoe]

I am still a bit inconsistent with how the assignments of numerical values that are represented as text in XML to enums should work. Anyway - got somewhere. Want to add some more tests and please direct me as you see fit.

[smoe]

@PoorRican , have added two tests - it now basically works. But more tests are needed as every test added somehow spotted an issue with naming of attributes or something else. :-)